As they develop in eggs exposed to the environment, fishes are especially susceptible to external influences during embryogenesis. These include temperature and light, which have been shown to have long-term fitness effects. In the SALMOCODE project, we use single-cell transcriptomics to investigate these vulnerabilities in the Atlantic salmon embryo.
In the first phase of this project, we have sampled eggs of farmed salmon between 124 and 238 day-degrees of development, corresponding to the interval between early organogenesis and the ‘eyed’ stage. By sampling every day, we have created a time lapse consisting of 23 developmental stages, which we have used for single-cell library preparation using the Parse Biosciences Evercode WT Mega kit. After sequencing, the current atlas contains data on 50000 cells, which belong to the approximately 50 broad cell types that emerge during early development.
In our main time lapse experiment, conducted at 4 °C, survival was high; however, in concurrent experiments at elevated temperatures, mortality was very high, and concentrated around specific developmental time points. We are currently profiling survivors of these bottlenecks using single-cell transcriptomics, under the hypothesis that they might show temperature-induced deviations from healthy organ development. These deviations could, in turn, have a negative impact on resilience later in life.
For the second phase of the project , we have sampled eggs more broadly between gastrulation and hatching, and under both controlled (4 °C, no light, commercial domesticated genetic background) and natural conditions (changing environmental conditions during the Norwegian winter, wild Atlantic salmon). After processing using single-cell transcriptomics, these will be combined with the phase one atlas to form a comprehensive, reuseable reference for early development.